[phenixbb] Fwd: Really good stats... Unreal!??
Pavel Afonine
pafonine at lbl.gov
Tue Oct 4 17:34:19 PDT 2011
Hi Yuri,
> So I am done refining a structure with around 760 residues in the
> model to a resolution of 2.29A. Rwork 0.18 Rfree 0.24
> RMSD angle 1.1 Bond 0.008, clashscore 28.
Looks ok to me, with some room for improvement (Rfree-Rwork gap,
clash-score).
> As a I last round I ran optmize_weights and got some interesting numbers.
> Rwork 0.17 Rfree 0.23
> RMSD Angle 0.68! Bond 0.003! clashscore 10.2
Looks even better! That's what weight optimization was supposed to do:
http://www.phenix-online.org/newsletter/
("Improved target weight optimization in phenix.refine")
Looking at R-factors for structures in PDB that are similar to yours:
Histogram of Rwork for models in PDB at resolution 2.19-2.39 A:
0.126 - 0.147 : 29
0.147 - 0.168 : 245
0.168 - 0.189 : 941 <<<< your structure
0.189 - 0.210 : 1613
0.210 - 0.232 : 1394
0.232 - 0.253 : 531
0.253 - 0.274 : 123
0.274 - 0.295 : 11
0.295 - 0.316 : 1
0.316 - 0.337 : 4
Histogram of Rfree for models in PDB at resolution 2.19-2.39 A:
0.165 - 0.188 : 31
0.188 - 0.211 : 220
0.211 - 0.235 : 848 <<<< your structure
0.235 - 0.258 : 1692
0.258 - 0.281 : 1459
0.281 - 0.304 : 522
0.304 - 0.328 : 94
0.328 - 0.351 : 19
0.351 - 0.374 : 6
0.374 - 0.397 : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.19-2.39 A:
0.001 - 0.011 : 51
0.011 - 0.021 : 170
0.021 - 0.031 : 509
0.031 - 0.041 : 944
0.041 - 0.050 : 1238
0.050 - 0.060 : 1017 <<<< your structure
0.060 - 0.070 : 574
0.070 - 0.080 : 214
0.080 - 0.090 : 110
0.090 - 0.100 : 65
Number of structures considered: 4892
Well, looks like just average!
Pavel
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